Starting phenix.real_space_refine on Wed Jun 11 10:00:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwv_29520/06_2025/8fwv_29520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwv_29520/06_2025/8fwv_29520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwv_29520/06_2025/8fwv_29520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwv_29520/06_2025/8fwv_29520.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwv_29520/06_2025/8fwv_29520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwv_29520/06_2025/8fwv_29520.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8004 2.51 5 N 2100 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12584 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.07, per 1000 atoms: 0.72 Number of scatterers: 12584 At special positions: 0 Unit cell: (104, 160.576, 85.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2412 8.00 N 2100 7.00 C 8004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 275 " " NAG C1002 " - " ASN C 412 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 67 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN B 67 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN D 378 " " NAG L 1 " - " ASN D 67 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 39.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.664A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.597A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.747A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 395 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU B 149 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLN B 131 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 149 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN C 131 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 149 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN D 131 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 395 428 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3741 1.33 - 1.45: 2114 1.45 - 1.57: 6882 1.57 - 1.69: 7 1.69 - 1.81: 120 Bond restraints: 12864 Sorted by residual: bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.659 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.647 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.645 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.530 -0.124 2.00e-02 2.50e+03 3.81e+01 ... (remaining 12859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 16711 2.38 - 4.75: 610 4.75 - 7.13: 81 7.13 - 9.50: 9 9.50 - 11.88: 9 Bond angle restraints: 17420 Sorted by residual: angle pdb=" N THR B 414 " pdb=" CA THR B 414 " pdb=" C THR B 414 " ideal model delta sigma weight residual 112.88 107.59 5.29 1.29e+00 6.01e-01 1.68e+01 angle pdb=" N THR C 414 " pdb=" CA THR C 414 " pdb=" C THR C 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR A 414 " pdb=" CA THR A 414 " pdb=" C THR A 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR D 414 " pdb=" CA THR D 414 " pdb=" C THR D 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " pdb=" C5 NAG D1002 " ideal model delta sigma weight residual 113.21 125.09 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 17415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 7718 23.14 - 46.27: 238 46.27 - 69.41: 48 69.41 - 92.54: 31 92.54 - 115.68: 25 Dihedral angle restraints: 8060 sinusoidal: 3592 harmonic: 4468 Sorted by residual: dihedral pdb=" CA GLY C 310 " pdb=" C GLY C 310 " pdb=" N LEU C 311 " pdb=" CA LEU C 311 " ideal model delta harmonic sigma weight residual -180.00 -119.43 -60.57 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY A 310 " pdb=" C GLY A 310 " pdb=" N LEU A 311 " pdb=" CA LEU A 311 " ideal model delta harmonic sigma weight residual -180.00 -119.44 -60.56 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" N LEU B 311 " pdb=" CA LEU B 311 " ideal model delta harmonic sigma weight residual 180.00 -119.49 -60.51 0 5.00e+00 4.00e-02 1.46e+02 ... (remaining 8057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.373: 2018 0.373 - 0.747: 2 0.747 - 1.120: 0 1.120 - 1.493: 0 1.493 - 1.866: 4 Chirality restraints: 2024 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 275 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.53 -1.87 2.00e-01 2.50e+01 8.71e+01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 275 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.60 -1.80 2.00e-01 2.50e+01 8.14e+01 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 275 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.16e+01 ... (remaining 2021 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 191 " -0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO B 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 191 " 0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO D 192 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 191 " -0.066 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.055 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4072 2.85 - 3.36: 10859 3.36 - 3.87: 20453 3.87 - 4.39: 23789 4.39 - 4.90: 41544 Nonbonded interactions: 100717 Sorted by model distance: nonbonded pdb=" OG1 THR A 173 " pdb=" OE1 GLU A 223 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLU B 223 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR D 173 " pdb=" OE1 GLU D 223 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR C 173 " pdb=" OE1 GLU C 223 " model vdw 2.335 3.040 nonbonded pdb=" OE1 GLU D 46 " pdb=" OG SER D 47 " model vdw 2.350 3.040 ... (remaining 100712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.850 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 12896 Z= 0.329 Angle : 1.238 29.065 17512 Z= 0.624 Chirality : 0.095 1.866 2024 Planarity : 0.008 0.100 2180 Dihedral : 14.818 115.681 5160 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.35 % Favored : 92.39 % Rotamer: Outliers : 1.19 % Allowed : 4.78 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.16), residues: 1524 helix: -4.16 (0.10), residues: 568 sheet: -2.50 (0.27), residues: 328 loop : -3.06 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 353 HIS 0.010 0.002 HIS A 253 PHE 0.024 0.003 PHE A 107 TYR 0.016 0.002 TYR D 252 ARG 0.008 0.001 ARG D 158 Details of bonding type rmsd link_NAG-ASN : bond 0.01481 ( 16) link_NAG-ASN : angle 10.18381 ( 48) link_BETA1-4 : bond 0.02842 ( 12) link_BETA1-4 : angle 7.57409 ( 36) hydrogen bonds : bond 0.28591 ( 428) hydrogen bonds : angle 9.69215 ( 1236) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.48138 ( 8) covalent geometry : bond 0.00717 (12864) covalent geometry : angle 1.06588 (17420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8632 (m) cc_final: 0.8192 (p) REVERT: A 156 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 222 LYS cc_start: 0.7945 (mttm) cc_final: 0.7691 (mmtm) REVERT: A 262 PHE cc_start: 0.7324 (t80) cc_final: 0.7036 (p90) REVERT: A 291 SER cc_start: 0.7469 (t) cc_final: 0.7240 (m) REVERT: A 360 MET cc_start: 0.7834 (tpt) cc_final: 0.7147 (tpt) REVERT: B 262 PHE cc_start: 0.7190 (t80) cc_final: 0.6935 (p90) REVERT: B 267 GLU cc_start: 0.7154 (tp30) cc_final: 0.6951 (tp30) REVERT: B 351 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7860 (mppt) REVERT: B 360 MET cc_start: 0.8370 (tpt) cc_final: 0.8166 (tpt) REVERT: C 113 SER cc_start: 0.8636 (m) cc_final: 0.8201 (p) REVERT: C 156 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (tp) REVERT: C 222 LYS cc_start: 0.7938 (mttm) cc_final: 0.7684 (mmtm) REVERT: C 262 PHE cc_start: 0.7303 (t80) cc_final: 0.7048 (p90) REVERT: C 291 SER cc_start: 0.7465 (t) cc_final: 0.7236 (m) REVERT: C 360 MET cc_start: 0.7832 (tpt) cc_final: 0.7148 (tpt) REVERT: D 152 ASP cc_start: 0.7924 (t0) cc_final: 0.7626 (t0) REVERT: D 198 ARG cc_start: 0.7350 (tmt-80) cc_final: 0.7052 (tpt90) REVERT: D 200 LYS cc_start: 0.7856 (mttp) cc_final: 0.7610 (mtpt) REVERT: D 247 MET cc_start: 0.9125 (mtp) cc_final: 0.8886 (mtp) REVERT: D 262 PHE cc_start: 0.7139 (t80) cc_final: 0.6876 (p90) REVERT: D 351 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7823 (mppt) outliers start: 16 outliers final: 4 residues processed: 325 average time/residue: 0.3343 time to fit residues: 145.6939 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 286 ASN A 335 GLN A 336 GLN A 346 GLN A 350 HIS ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 335 GLN B 336 GLN B 350 HIS C 196 ASN C 286 ASN C 335 GLN C 336 GLN C 346 GLN C 350 HIS D 288 GLN D 335 GLN D 336 GLN D 350 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135958 restraints weight = 13425.022| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.22 r_work: 0.3316 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12896 Z= 0.172 Angle : 0.850 23.369 17512 Z= 0.385 Chirality : 0.060 1.100 2024 Planarity : 0.006 0.084 2180 Dihedral : 12.755 83.646 2244 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.88 % Allowed : 9.70 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.18), residues: 1524 helix: -2.26 (0.17), residues: 568 sheet: -2.46 (0.27), residues: 328 loop : -2.73 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 353 HIS 0.007 0.001 HIS D 253 PHE 0.015 0.002 PHE B 107 TYR 0.008 0.001 TYR B 252 ARG 0.005 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.01102 ( 16) link_NAG-ASN : angle 6.97394 ( 48) link_BETA1-4 : bond 0.02510 ( 12) link_BETA1-4 : angle 5.01330 ( 36) hydrogen bonds : bond 0.04423 ( 428) hydrogen bonds : angle 4.93149 ( 1236) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.43454 ( 8) covalent geometry : bond 0.00387 (12864) covalent geometry : angle 0.73519 (17420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7031 (mm) REVERT: A 113 SER cc_start: 0.8844 (m) cc_final: 0.8489 (p) REVERT: A 156 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8014 (mt) REVERT: A 177 ASP cc_start: 0.8330 (t70) cc_final: 0.8087 (t0) REVERT: A 222 LYS cc_start: 0.8089 (mttm) cc_final: 0.7668 (mmtm) REVERT: A 262 PHE cc_start: 0.7797 (t80) cc_final: 0.7139 (p90) REVERT: A 291 SER cc_start: 0.7649 (t) cc_final: 0.7360 (m) REVERT: A 360 MET cc_start: 0.7946 (tpt) cc_final: 0.7431 (tpt) REVERT: B 262 PHE cc_start: 0.7978 (t80) cc_final: 0.7109 (p90) REVERT: B 288 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7624 (mm110) REVERT: B 351 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7937 (mppt) REVERT: C 55 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7048 (mm) REVERT: C 113 SER cc_start: 0.8834 (m) cc_final: 0.8480 (p) REVERT: C 156 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8008 (mt) REVERT: C 177 ASP cc_start: 0.8355 (t70) cc_final: 0.8115 (t0) REVERT: C 222 LYS cc_start: 0.8081 (mttm) cc_final: 0.7657 (mmtm) REVERT: C 262 PHE cc_start: 0.7788 (t80) cc_final: 0.7110 (p90) REVERT: C 291 SER cc_start: 0.7652 (t) cc_final: 0.7369 (m) REVERT: C 360 MET cc_start: 0.7909 (tpt) cc_final: 0.7402 (tpt) REVERT: D 81 GLN cc_start: 0.8557 (mt0) cc_final: 0.8304 (mt0) REVERT: D 198 ARG cc_start: 0.7941 (tmt-80) cc_final: 0.7479 (tpt90) REVERT: D 218 MET cc_start: 0.8965 (mtp) cc_final: 0.8702 (mtm) REVERT: D 247 MET cc_start: 0.9219 (mtp) cc_final: 0.8978 (mtp) REVERT: D 262 PHE cc_start: 0.7972 (t80) cc_final: 0.7099 (p90) REVERT: D 351 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7709 (mppt) outliers start: 52 outliers final: 25 residues processed: 204 average time/residue: 0.3997 time to fit residues: 117.4024 Evaluate side-chains 179 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 346 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 346 GLN D 98 GLN D 165 GLN D 288 GLN D 346 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131782 restraints weight = 13590.856| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.33 r_work: 0.3257 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12896 Z= 0.217 Angle : 0.833 23.022 17512 Z= 0.373 Chirality : 0.062 1.071 2024 Planarity : 0.006 0.080 2180 Dihedral : 10.084 59.677 2244 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.10 % Allowed : 9.18 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.19), residues: 1524 helix: -0.70 (0.19), residues: 576 sheet: -2.32 (0.27), residues: 332 loop : -2.77 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 296 HIS 0.008 0.001 HIS D 253 PHE 0.018 0.003 PHE D 377 TYR 0.017 0.002 TYR C 195 ARG 0.004 0.000 ARG D 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00939 ( 16) link_NAG-ASN : angle 6.45650 ( 48) link_BETA1-4 : bond 0.02059 ( 12) link_BETA1-4 : angle 4.73906 ( 36) hydrogen bonds : bond 0.04027 ( 428) hydrogen bonds : angle 4.36028 ( 1236) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.22387 ( 8) covalent geometry : bond 0.00519 (12864) covalent geometry : angle 0.73261 (17420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7051 (mm) REVERT: A 113 SER cc_start: 0.8783 (m) cc_final: 0.8386 (p) REVERT: A 156 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7855 (mm) REVERT: A 160 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 220 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7608 (mtm110) REVERT: A 222 LYS cc_start: 0.8099 (mttm) cc_final: 0.7648 (mmtm) REVERT: A 262 PHE cc_start: 0.7895 (t80) cc_final: 0.7053 (p90) REVERT: A 291 SER cc_start: 0.7749 (t) cc_final: 0.7428 (m) REVERT: A 298 MET cc_start: 0.6476 (tmm) cc_final: 0.6254 (tmm) REVERT: A 400 GLU cc_start: 0.7628 (tt0) cc_final: 0.6900 (mm-30) REVERT: B 50 MET cc_start: 0.7545 (ptp) cc_final: 0.7268 (ptt) REVERT: B 262 PHE cc_start: 0.8205 (t80) cc_final: 0.7125 (p90) REVERT: B 288 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7595 (mm110) REVERT: B 351 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7975 (mptt) REVERT: C 55 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7053 (mm) REVERT: C 113 SER cc_start: 0.8786 (m) cc_final: 0.8360 (p) REVERT: C 156 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7849 (mm) REVERT: C 160 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8353 (mp) REVERT: C 220 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7635 (mtm110) REVERT: C 222 LYS cc_start: 0.8098 (mttm) cc_final: 0.7652 (mmtm) REVERT: C 262 PHE cc_start: 0.7903 (t80) cc_final: 0.7025 (p90) REVERT: C 291 SER cc_start: 0.7787 (t) cc_final: 0.7469 (m) REVERT: C 298 MET cc_start: 0.6475 (tmm) cc_final: 0.6255 (tmm) REVERT: C 400 GLU cc_start: 0.7613 (tt0) cc_final: 0.6882 (mm-30) REVERT: D 50 MET cc_start: 0.7543 (ptp) cc_final: 0.7260 (ptt) REVERT: D 81 GLN cc_start: 0.8579 (mt0) cc_final: 0.8358 (mt0) REVERT: D 198 ARG cc_start: 0.7896 (tmt-80) cc_final: 0.7418 (tpt90) REVERT: D 218 MET cc_start: 0.9059 (mtp) cc_final: 0.8770 (mtm) REVERT: D 262 PHE cc_start: 0.8200 (t80) cc_final: 0.7131 (p90) REVERT: D 288 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7589 (mm-40) REVERT: D 351 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7899 (mppt) outliers start: 55 outliers final: 31 residues processed: 207 average time/residue: 0.3423 time to fit residues: 101.9031 Evaluate side-chains 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132889 restraints weight = 13560.785| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.41 r_work: 0.3271 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12896 Z= 0.156 Angle : 0.783 22.528 17512 Z= 0.346 Chirality : 0.060 1.091 2024 Planarity : 0.005 0.076 2180 Dihedral : 8.796 55.549 2244 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.66 % Allowed : 10.60 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1524 helix: 0.12 (0.21), residues: 572 sheet: -2.22 (0.27), residues: 332 loop : -2.68 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 296 HIS 0.005 0.001 HIS D 253 PHE 0.014 0.002 PHE B 107 TYR 0.025 0.002 TYR C 195 ARG 0.002 0.000 ARG B 384 Details of bonding type rmsd link_NAG-ASN : bond 0.01050 ( 16) link_NAG-ASN : angle 6.80283 ( 48) link_BETA1-4 : bond 0.02024 ( 12) link_BETA1-4 : angle 4.58303 ( 36) hydrogen bonds : bond 0.03411 ( 428) hydrogen bonds : angle 4.12042 ( 1236) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.63484 ( 8) covalent geometry : bond 0.00363 (12864) covalent geometry : angle 0.66751 (17420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7041 (mm) REVERT: A 113 SER cc_start: 0.8835 (m) cc_final: 0.8425 (p) REVERT: A 160 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 220 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7768 (mtm110) REVERT: A 222 LYS cc_start: 0.8119 (mttm) cc_final: 0.7581 (mtmt) REVERT: A 262 PHE cc_start: 0.7940 (t80) cc_final: 0.7084 (p90) REVERT: A 360 MET cc_start: 0.8006 (tpt) cc_final: 0.7538 (tpt) REVERT: A 400 GLU cc_start: 0.7640 (tt0) cc_final: 0.6920 (mm-30) REVERT: B 262 PHE cc_start: 0.8251 (t80) cc_final: 0.7153 (p90) REVERT: B 288 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7609 (mm110) REVERT: B 351 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7975 (mptt) REVERT: C 55 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7063 (mm) REVERT: C 113 SER cc_start: 0.8806 (m) cc_final: 0.8390 (p) REVERT: C 160 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 220 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7794 (mtm110) REVERT: C 222 LYS cc_start: 0.8117 (mttm) cc_final: 0.7587 (mtmt) REVERT: C 262 PHE cc_start: 0.7934 (t80) cc_final: 0.7050 (p90) REVERT: C 400 GLU cc_start: 0.7636 (tt0) cc_final: 0.6915 (mm-30) REVERT: D 198 ARG cc_start: 0.7895 (tmt-80) cc_final: 0.7468 (tpt90) REVERT: D 218 MET cc_start: 0.9058 (mtp) cc_final: 0.8805 (mtm) REVERT: D 262 PHE cc_start: 0.8237 (t80) cc_final: 0.7171 (p90) REVERT: D 288 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7537 (mm-40) REVERT: D 351 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7857 (mppt) outliers start: 49 outliers final: 32 residues processed: 204 average time/residue: 0.2503 time to fit residues: 73.0213 Evaluate side-chains 189 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 0.0270 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134022 restraints weight = 13577.159| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.40 r_work: 0.3273 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12896 Z= 0.136 Angle : 0.746 20.986 17512 Z= 0.329 Chirality : 0.059 1.131 2024 Planarity : 0.005 0.076 2180 Dihedral : 7.773 49.629 2240 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.88 % Allowed : 11.04 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1524 helix: 0.72 (0.22), residues: 568 sheet: -2.11 (0.29), residues: 292 loop : -2.56 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 296 HIS 0.005 0.001 HIS D 253 PHE 0.013 0.002 PHE D 107 TYR 0.013 0.001 TYR C 195 ARG 0.006 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.01036 ( 16) link_NAG-ASN : angle 6.26482 ( 48) link_BETA1-4 : bond 0.01924 ( 12) link_BETA1-4 : angle 4.45497 ( 36) hydrogen bonds : bond 0.03236 ( 428) hydrogen bonds : angle 4.00688 ( 1236) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.14901 ( 8) covalent geometry : bond 0.00309 (12864) covalent geometry : angle 0.64012 (17420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7046 (mm) REVERT: A 113 SER cc_start: 0.8777 (m) cc_final: 0.8347 (p) REVERT: A 160 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8251 (mp) REVERT: A 222 LYS cc_start: 0.8090 (mttm) cc_final: 0.7782 (mmtt) REVERT: A 262 PHE cc_start: 0.8125 (t80) cc_final: 0.7057 (p90) REVERT: A 275 ASN cc_start: 0.5322 (m-40) cc_final: 0.5101 (m-40) REVERT: A 283 ASN cc_start: 0.7172 (t0) cc_final: 0.6919 (t0) REVERT: A 400 GLU cc_start: 0.7626 (tt0) cc_final: 0.6874 (mm-30) REVERT: B 262 PHE cc_start: 0.8296 (t80) cc_final: 0.7160 (p90) REVERT: B 288 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7610 (mm110) REVERT: B 351 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7948 (mppt) REVERT: C 55 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7053 (mm) REVERT: C 113 SER cc_start: 0.8760 (m) cc_final: 0.8319 (p) REVERT: C 160 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8255 (mp) REVERT: C 222 LYS cc_start: 0.8087 (mttm) cc_final: 0.7783 (mmtt) REVERT: C 262 PHE cc_start: 0.8120 (t80) cc_final: 0.7029 (p90) REVERT: C 275 ASN cc_start: 0.5289 (m-40) cc_final: 0.5046 (m-40) REVERT: C 283 ASN cc_start: 0.7204 (t0) cc_final: 0.6938 (t0) REVERT: C 400 GLU cc_start: 0.7634 (tt0) cc_final: 0.6889 (mm-30) REVERT: D 198 ARG cc_start: 0.7863 (tmt-80) cc_final: 0.7430 (tpt90) REVERT: D 218 MET cc_start: 0.9031 (mtp) cc_final: 0.8799 (mtm) REVERT: D 262 PHE cc_start: 0.8280 (t80) cc_final: 0.7145 (p90) REVERT: D 288 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7446 (mm-40) REVERT: D 351 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7770 (mppt) outliers start: 52 outliers final: 38 residues processed: 202 average time/residue: 0.2485 time to fit residues: 71.8686 Evaluate side-chains 193 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 0.4980 chunk 141 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 98 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.173842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134369 restraints weight = 13642.685| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.40 r_work: 0.3288 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12896 Z= 0.131 Angle : 0.711 20.017 17512 Z= 0.317 Chirality : 0.055 0.963 2024 Planarity : 0.005 0.072 2180 Dihedral : 7.212 50.197 2240 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.28 % Allowed : 12.09 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1524 helix: 1.20 (0.22), residues: 572 sheet: -2.02 (0.29), residues: 292 loop : -2.49 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 296 HIS 0.004 0.001 HIS A 253 PHE 0.014 0.001 PHE A 107 TYR 0.024 0.001 TYR B 86 ARG 0.005 0.000 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 16) link_NAG-ASN : angle 5.67740 ( 48) link_BETA1-4 : bond 0.01881 ( 12) link_BETA1-4 : angle 4.37573 ( 36) hydrogen bonds : bond 0.03002 ( 428) hydrogen bonds : angle 3.88138 ( 1236) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.13238 ( 8) covalent geometry : bond 0.00299 (12864) covalent geometry : angle 0.61647 (17420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7140 (mm) REVERT: A 113 SER cc_start: 0.8763 (m) cc_final: 0.8320 (p) REVERT: A 160 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8269 (mp) REVERT: A 222 LYS cc_start: 0.8079 (mttm) cc_final: 0.7530 (mtmt) REVERT: A 262 PHE cc_start: 0.8146 (t80) cc_final: 0.7080 (p90) REVERT: A 283 ASN cc_start: 0.7181 (t0) cc_final: 0.6951 (t0) REVERT: A 335 GLN cc_start: 0.6803 (tp40) cc_final: 0.6519 (tt0) REVERT: A 351 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7813 (mptt) REVERT: B 200 LYS cc_start: 0.8452 (mttp) cc_final: 0.8231 (mttt) REVERT: B 262 PHE cc_start: 0.8343 (t80) cc_final: 0.7203 (p90) REVERT: B 288 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7628 (mm110) REVERT: B 351 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7938 (mppt) REVERT: C 55 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7170 (mm) REVERT: C 160 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8272 (mp) REVERT: C 222 LYS cc_start: 0.8071 (mttm) cc_final: 0.7526 (mtmt) REVERT: C 262 PHE cc_start: 0.8112 (t80) cc_final: 0.7052 (p90) REVERT: C 283 ASN cc_start: 0.7223 (t0) cc_final: 0.6991 (t0) REVERT: C 335 GLN cc_start: 0.6803 (tp40) cc_final: 0.6512 (tt0) REVERT: C 351 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7839 (mptt) REVERT: D 198 ARG cc_start: 0.7906 (tmt-80) cc_final: 0.7484 (tpt90) REVERT: D 218 MET cc_start: 0.9028 (mtp) cc_final: 0.8801 (mtm) REVERT: D 262 PHE cc_start: 0.8328 (t80) cc_final: 0.7191 (p90) REVERT: D 288 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7444 (mm-40) REVERT: D 351 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7725 (mppt) outliers start: 44 outliers final: 30 residues processed: 182 average time/residue: 0.2413 time to fit residues: 63.9745 Evaluate side-chains 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 147 optimal weight: 0.0570 chunk 150 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137905 restraints weight = 13533.843| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.26 r_work: 0.3335 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12896 Z= 0.120 Angle : 0.752 23.479 17512 Z= 0.325 Chirality : 0.051 0.948 2024 Planarity : 0.005 0.072 2180 Dihedral : 7.111 51.061 2240 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.91 % Allowed : 12.16 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1524 helix: 1.48 (0.22), residues: 572 sheet: -1.92 (0.29), residues: 292 loop : -2.39 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 296 HIS 0.003 0.000 HIS D 253 PHE 0.011 0.001 PHE D 107 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00954 ( 16) link_NAG-ASN : angle 7.52827 ( 48) link_BETA1-4 : bond 0.01832 ( 12) link_BETA1-4 : angle 4.27580 ( 36) hydrogen bonds : bond 0.02823 ( 428) hydrogen bonds : angle 3.79893 ( 1236) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.11634 ( 8) covalent geometry : bond 0.00268 (12864) covalent geometry : angle 0.61259 (17420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7215 (mm) REVERT: A 113 SER cc_start: 0.8775 (m) cc_final: 0.8331 (p) REVERT: A 160 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 195 TYR cc_start: 0.6740 (m-10) cc_final: 0.6537 (m-10) REVERT: A 222 LYS cc_start: 0.8160 (mttm) cc_final: 0.7863 (mmtt) REVERT: A 262 PHE cc_start: 0.8135 (t80) cc_final: 0.7113 (p90) REVERT: A 283 ASN cc_start: 0.7204 (t0) cc_final: 0.6515 (m-40) REVERT: A 335 GLN cc_start: 0.6822 (tp40) cc_final: 0.6558 (tt0) REVERT: A 351 LYS cc_start: 0.8088 (mtmm) cc_final: 0.7793 (mptt) REVERT: B 50 MET cc_start: 0.7659 (ptt) cc_final: 0.7265 (ptt) REVERT: B 200 LYS cc_start: 0.8446 (mttp) cc_final: 0.8238 (mttt) REVERT: B 262 PHE cc_start: 0.8357 (t80) cc_final: 0.7236 (p90) REVERT: B 288 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7616 (mm110) REVERT: B 351 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7939 (mppt) REVERT: C 55 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7214 (mm) REVERT: C 160 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8274 (mp) REVERT: C 222 LYS cc_start: 0.8169 (mttm) cc_final: 0.7657 (mtmt) REVERT: C 262 PHE cc_start: 0.8122 (t80) cc_final: 0.7086 (p90) REVERT: C 283 ASN cc_start: 0.7227 (t0) cc_final: 0.6534 (m-40) REVERT: C 335 GLN cc_start: 0.6824 (tp40) cc_final: 0.6555 (tt0) REVERT: C 351 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7819 (mptt) REVERT: D 50 MET cc_start: 0.7658 (ptt) cc_final: 0.7252 (ptt) REVERT: D 198 ARG cc_start: 0.7935 (tmt-80) cc_final: 0.7505 (tpt90) REVERT: D 200 LYS cc_start: 0.8508 (mttp) cc_final: 0.8280 (mttt) REVERT: D 218 MET cc_start: 0.9009 (mtp) cc_final: 0.8778 (mtm) REVERT: D 262 PHE cc_start: 0.8382 (t80) cc_final: 0.7261 (p90) REVERT: D 288 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7468 (mm-40) REVERT: D 351 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7717 (mppt) outliers start: 39 outliers final: 32 residues processed: 185 average time/residue: 0.2538 time to fit residues: 67.3152 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135627 restraints weight = 13630.529| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.33 r_work: 0.3299 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12896 Z= 0.161 Angle : 0.729 19.583 17512 Z= 0.324 Chirality : 0.053 0.896 2024 Planarity : 0.005 0.071 2180 Dihedral : 6.980 49.184 2240 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.21 % Allowed : 12.46 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1524 helix: 1.42 (0.22), residues: 572 sheet: -1.99 (0.28), residues: 312 loop : -2.35 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 296 HIS 0.003 0.001 HIS B 232 PHE 0.014 0.002 PHE D 107 TYR 0.024 0.001 TYR B 86 ARG 0.008 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00922 ( 16) link_NAG-ASN : angle 6.37288 ( 48) link_BETA1-4 : bond 0.01738 ( 12) link_BETA1-4 : angle 4.23979 ( 36) hydrogen bonds : bond 0.02975 ( 428) hydrogen bonds : angle 3.85666 ( 1236) SS BOND : bond 0.00031 ( 4) SS BOND : angle 0.14167 ( 8) covalent geometry : bond 0.00383 (12864) covalent geometry : angle 0.62121 (17420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7454 (mt) REVERT: A 160 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8272 (mp) REVERT: A 222 LYS cc_start: 0.8201 (mttm) cc_final: 0.7674 (mtmt) REVERT: A 262 PHE cc_start: 0.8190 (t80) cc_final: 0.7150 (p90) REVERT: A 283 ASN cc_start: 0.7187 (t0) cc_final: 0.6976 (t0) REVERT: A 335 GLN cc_start: 0.6802 (tp40) cc_final: 0.6554 (tt0) REVERT: A 351 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7819 (mptt) REVERT: B 200 LYS cc_start: 0.8505 (mttp) cc_final: 0.8261 (mttt) REVERT: B 234 MET cc_start: 0.9015 (ttm) cc_final: 0.8812 (mtp) REVERT: B 262 PHE cc_start: 0.8473 (t80) cc_final: 0.7289 (p90) REVERT: B 288 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7641 (mm110) REVERT: B 351 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7853 (mppt) REVERT: C 55 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7437 (mt) REVERT: C 160 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8264 (mp) REVERT: C 222 LYS cc_start: 0.8129 (mttm) cc_final: 0.7590 (mtmt) REVERT: C 262 PHE cc_start: 0.8184 (t80) cc_final: 0.7134 (p90) REVERT: C 283 ASN cc_start: 0.7210 (t0) cc_final: 0.6999 (t0) REVERT: C 335 GLN cc_start: 0.6808 (tp40) cc_final: 0.6547 (tt0) REVERT: C 351 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7813 (mptt) REVERT: D 198 ARG cc_start: 0.7973 (tmt-80) cc_final: 0.7523 (tpt90) REVERT: D 200 LYS cc_start: 0.8575 (mttp) cc_final: 0.8317 (mttt) REVERT: D 218 MET cc_start: 0.9035 (mtp) cc_final: 0.8760 (mtm) REVERT: D 262 PHE cc_start: 0.8463 (t80) cc_final: 0.7260 (p90) REVERT: D 288 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7499 (mm-40) REVERT: D 351 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7789 (mptt) outliers start: 43 outliers final: 36 residues processed: 187 average time/residue: 0.2665 time to fit residues: 72.7147 Evaluate side-chains 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 105 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 132 optimal weight: 0.0470 chunk 129 optimal weight: 1.9990 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139488 restraints weight = 13434.154| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.14 r_work: 0.3371 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12896 Z= 0.101 Angle : 0.655 17.913 17512 Z= 0.294 Chirality : 0.049 0.805 2024 Planarity : 0.004 0.070 2180 Dihedral : 6.448 50.706 2240 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.31 % Allowed : 12.99 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1524 helix: 1.85 (0.22), residues: 572 sheet: -1.71 (0.29), residues: 292 loop : -2.29 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 296 HIS 0.003 0.000 HIS D 253 PHE 0.008 0.001 PHE D 59 TYR 0.033 0.001 TYR B 86 ARG 0.007 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00911 ( 16) link_NAG-ASN : angle 5.54234 ( 48) link_BETA1-4 : bond 0.01738 ( 12) link_BETA1-4 : angle 3.95459 ( 36) hydrogen bonds : bond 0.02639 ( 428) hydrogen bonds : angle 3.73850 ( 1236) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.12220 ( 8) covalent geometry : bond 0.00209 (12864) covalent geometry : angle 0.56108 (17420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7691 (mm) cc_final: 0.7452 (mt) REVERT: A 196 ASN cc_start: 0.8087 (t0) cc_final: 0.7709 (t0) REVERT: A 222 LYS cc_start: 0.8137 (mttm) cc_final: 0.7622 (mtmt) REVERT: A 262 PHE cc_start: 0.8279 (t80) cc_final: 0.7200 (p90) REVERT: A 283 ASN cc_start: 0.7017 (t0) cc_final: 0.6523 (p0) REVERT: A 335 GLN cc_start: 0.6759 (tp40) cc_final: 0.6517 (tt0) REVERT: A 351 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7820 (mptt) REVERT: A 360 MET cc_start: 0.7918 (tpt) cc_final: 0.7717 (tpt) REVERT: B 50 MET cc_start: 0.7394 (ptt) cc_final: 0.7021 (ptt) REVERT: B 133 ARG cc_start: 0.8784 (ttt-90) cc_final: 0.8331 (mtp85) REVERT: B 200 LYS cc_start: 0.8421 (mttp) cc_final: 0.8184 (mttt) REVERT: B 234 MET cc_start: 0.8969 (ttm) cc_final: 0.8749 (mtp) REVERT: B 262 PHE cc_start: 0.8433 (t80) cc_final: 0.7266 (p90) REVERT: B 288 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7619 (mm110) REVERT: B 351 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7867 (mppt) REVERT: C 55 LEU cc_start: 0.7705 (mm) cc_final: 0.7463 (mt) REVERT: C 196 ASN cc_start: 0.8067 (t0) cc_final: 0.7722 (t0) REVERT: C 222 LYS cc_start: 0.8141 (mttm) cc_final: 0.7855 (mmtt) REVERT: C 262 PHE cc_start: 0.8262 (t80) cc_final: 0.7220 (p90) REVERT: C 283 ASN cc_start: 0.7097 (t0) cc_final: 0.6564 (p0) REVERT: C 335 GLN cc_start: 0.6784 (tp40) cc_final: 0.6534 (tt0) REVERT: C 351 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7819 (mptt) REVERT: D 50 MET cc_start: 0.7406 (ptt) cc_final: 0.7030 (ptt) REVERT: D 133 ARG cc_start: 0.8772 (ttt-90) cc_final: 0.8305 (mtp85) REVERT: D 198 ARG cc_start: 0.7901 (tmt-80) cc_final: 0.7493 (tpt90) REVERT: D 200 LYS cc_start: 0.8508 (mttp) cc_final: 0.8273 (mttt) REVERT: D 262 PHE cc_start: 0.8465 (t80) cc_final: 0.7305 (p90) REVERT: D 288 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7446 (mm-40) REVERT: D 351 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7703 (mptt) outliers start: 31 outliers final: 26 residues processed: 183 average time/residue: 0.2840 time to fit residues: 74.8329 Evaluate side-chains 175 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 0.0570 chunk 52 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN D 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138219 restraints weight = 13472.736| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.31 r_work: 0.3340 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12896 Z= 0.128 Angle : 0.658 17.776 17512 Z= 0.301 Chirality : 0.048 0.739 2024 Planarity : 0.005 0.074 2180 Dihedral : 7.168 86.356 2240 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.24 % Allowed : 13.73 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1524 helix: 1.80 (0.22), residues: 572 sheet: -1.65 (0.29), residues: 292 loop : -2.25 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 296 HIS 0.026 0.001 HIS A 253 PHE 0.013 0.001 PHE B 107 TYR 0.021 0.001 TYR B 86 ARG 0.006 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00913 ( 16) link_NAG-ASN : angle 4.58701 ( 48) link_BETA1-4 : bond 0.01720 ( 12) link_BETA1-4 : angle 3.96298 ( 36) hydrogen bonds : bond 0.02665 ( 428) hydrogen bonds : angle 3.84455 ( 1236) SS BOND : bond 0.00038 ( 4) SS BOND : angle 0.15011 ( 8) covalent geometry : bond 0.00292 (12864) covalent geometry : angle 0.58686 (17420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7715 (mm) cc_final: 0.7480 (mt) REVERT: A 194 ARG cc_start: 0.7715 (mtp180) cc_final: 0.7472 (ptm160) REVERT: A 196 ASN cc_start: 0.8072 (t0) cc_final: 0.7689 (t0) REVERT: A 222 LYS cc_start: 0.8184 (mttm) cc_final: 0.7661 (mtmt) REVERT: A 262 PHE cc_start: 0.8305 (t80) cc_final: 0.7233 (p90) REVERT: A 283 ASN cc_start: 0.7083 (t0) cc_final: 0.6559 (p0) REVERT: A 335 GLN cc_start: 0.6813 (tp40) cc_final: 0.6539 (tt0) REVERT: A 351 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7836 (mptt) REVERT: A 360 MET cc_start: 0.7606 (tpt) cc_final: 0.7042 (tpt) REVERT: B 50 MET cc_start: 0.7434 (ptt) cc_final: 0.7057 (ptt) REVERT: B 133 ARG cc_start: 0.8822 (ttt-90) cc_final: 0.8358 (mtp85) REVERT: B 200 LYS cc_start: 0.8454 (mttp) cc_final: 0.8188 (mttt) REVERT: B 234 MET cc_start: 0.8992 (ttm) cc_final: 0.8775 (mtp) REVERT: B 262 PHE cc_start: 0.8425 (t80) cc_final: 0.7268 (p90) REVERT: B 288 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7650 (mm110) REVERT: B 351 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7850 (mppt) REVERT: C 55 LEU cc_start: 0.7717 (mm) cc_final: 0.7482 (mt) REVERT: C 194 ARG cc_start: 0.7701 (mtp180) cc_final: 0.7471 (ptm160) REVERT: C 196 ASN cc_start: 0.8048 (t0) cc_final: 0.7693 (t0) REVERT: C 222 LYS cc_start: 0.8192 (mttm) cc_final: 0.7666 (mtmt) REVERT: C 262 PHE cc_start: 0.8284 (t80) cc_final: 0.7225 (p90) REVERT: C 283 ASN cc_start: 0.7112 (t0) cc_final: 0.6576 (p0) REVERT: C 335 GLN cc_start: 0.6828 (tp40) cc_final: 0.6548 (tt0) REVERT: C 351 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7848 (mptt) REVERT: C 360 MET cc_start: 0.7632 (tpt) cc_final: 0.7030 (tpt) REVERT: D 50 MET cc_start: 0.7450 (ptt) cc_final: 0.7080 (ptt) REVERT: D 198 ARG cc_start: 0.7952 (tmt-80) cc_final: 0.7515 (tpt90) REVERT: D 200 LYS cc_start: 0.8570 (mttp) cc_final: 0.8293 (mttt) REVERT: D 262 PHE cc_start: 0.8455 (t80) cc_final: 0.7279 (p90) REVERT: D 288 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7472 (mm-40) REVERT: D 351 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7766 (mptt) outliers start: 30 outliers final: 26 residues processed: 177 average time/residue: 0.2982 time to fit residues: 75.8961 Evaluate side-chains 178 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.0020 chunk 85 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136987 restraints weight = 13592.574| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.39 r_work: 0.3326 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12896 Z= 0.125 Angle : 0.648 17.508 17512 Z= 0.298 Chirality : 0.047 0.731 2024 Planarity : 0.005 0.074 2180 Dihedral : 6.667 62.014 2240 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.54 % Allowed : 13.58 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1524 helix: 1.81 (0.22), residues: 572 sheet: -1.55 (0.30), residues: 292 loop : -2.17 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 296 HIS 0.014 0.001 HIS A 253 PHE 0.012 0.001 PHE D 107 TYR 0.023 0.001 TYR B 86 ARG 0.006 0.000 ARG D 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00819 ( 16) link_NAG-ASN : angle 4.62825 ( 48) link_BETA1-4 : bond 0.01641 ( 12) link_BETA1-4 : angle 3.85382 ( 36) hydrogen bonds : bond 0.02706 ( 428) hydrogen bonds : angle 3.83418 ( 1236) SS BOND : bond 0.00031 ( 4) SS BOND : angle 0.14549 ( 8) covalent geometry : bond 0.00286 (12864) covalent geometry : angle 0.57656 (17420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9589.82 seconds wall clock time: 171 minutes 41.96 seconds (10301.96 seconds total)